" I have a big problem with a defense being able to play nickel/pass and shut down a good running game, it's simply not realistic."
The simple fact that teams don't run out of the shotgun proves it IS realistic.
If your a team facing an offense that runs out of the shotgun-you place 2 stout DTs to occupy the 2 guards and the center, you have 2 stout DEs to occupy both OTs, that leaves one TE to block and free the QB from 2 LB's? NOPE, the runs aren't going anywhere.
As for the real life college QB's like Young, Vick, Tebow etc.-are you argueing that they only ran out of the shotgun. I'm not a fan of Tebow and didn't watch him very often, but I don't recall him running out the shotgun (other than a scramble). There were running plays, but they were more an option play-give to the RB or keep for himself (if I'm wrong tell me).
Now in Brava, the leading rusher was a QB-in many of the games he was getting 60 pr 70 runs per game.
IN REAL LIFE-in 2012, RB Montee Ball averaged 24.5 rushes per game, but in GD 3.0, a QB should be able to rush 60 to 70 times a game? That's realistic?
Getting back to Tebow or Young-how many pure rushes did they actually make? How many pure rushes out of the shotgun (I would wager 0 times out of the shotgun)? I would hazard a guess that actual pure runs by Tebow/Young etc were about 10/gm max (not including scrambles when flushed fom the pocket during a pass play). If they were running in the 20's or 30's, defensive players wouldn't need to make the tackle, they could just step on the QB's tongue, because by that point the QBs tongues would be dragging on the ground.
It would seem to me the easiest fix would be to have QB runs/scramble (from the pocket) have a significant drain on a QB's stamina. I think this would have the desired effect without having to curb the yards gained by a QB. You may even be able to increase gains made on a run/scramble by the QB-but ot the detriment of playing time for the QB.